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Persistent homology

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https://www.readbyqxmd.com/read/28923592/comparative-study-of-three-c1q-domain-containing-proteins-from-pacific-oyster-crassostrea-gigas
#1
Zhao Lv, Limei Qiu, Mengqiang Wang, Zhihao Jia, Weilin Wang, Lusheng Xin, Zhaoqun Liu, Lingling Wang, Linsheng Song
C1q domain containing proteins (C1qDCs) are a family of proteins containing a globular head C1q domain (ghC1q) in C-terminus, which serve as pattern recognition receptors (PRRs) and mediate a series of immune responses. In the present study, three C1qDC proteins from Pacific oyster Crassostrea gigas (CgC1qDC-2, CgC1qDC-3, CgC1qDC-4) were characterized and comparatively investigated to understand their roles in the immune response. All the three recombinant CgC1qDC proteins (rCgC1qDCs) could bind lipopolysaccharide (LPS) significantly but they could not bind lipoteichoic acid (LTA), β-1,3-glucan (GLU), mannan (MAN), and polyinosinic-polycytidylic acid (Poly I:C)...
September 16, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28922851/%C3%AE-endosulfine-arpp-19e-expression-in-a-rat-model-of-stroke
#2
Rupal I Mehta, Natalia Tsymbalyuk, Svetlana Ivanova, Jesse A Stokum, Kyoon Woo, Volodymyr Gerzanich, J Marc Simard
In nutrient restricted environments, the yeast endosulfines Igo1/2 are activated via TORC1 inhibition and function critically to initiate and coordinate the cellular stress response that promotes survival. We examined expression of αEnsa, the mammalian homolog of yeast endosulfines, in rat stroke. Prominent neuronal upregulation of αEnsa was identified in 3 patterns within the ischemic gradient: (1) neurons in GFAP-/HSF1+ cortex showed upregulation and near-complete nuclear translocation of αEnsa protein within hours of ischemic onset; (2) neurons in GFAP+/HSF1+ cortex showed upregulation in cytoplasm and nuclei that persisted for days; (3) neurons in GFAP+/HSF1- cortex showed delayed cytosolic-only upregulation that persisted for days...
October 1, 2017: Journal of Neuropathology and Experimental Neurology
https://www.readbyqxmd.com/read/28922417/lingering-single-strand-breaks-trigger-rad51-independent-homology-directed-repair-of-collapsed-replication-forks-in-the-polynucleotide-kinase-phosphatase-mutant-of-fission-yeast
#3
Arancha Sanchez, Mariana C Gadaleta, Oliver Limbo, Paul Russell
The DNA repair enzyme polynucleotide kinase/phosphatase (PNKP) protects genome integrity by restoring ligatable 5'-phosphate and 3'-hydroxyl termini at single-strand breaks (SSBs). In humans, PNKP mutations underlie the neurological disease known as MCSZ, but these individuals are not predisposed for cancer, implying effective alternative repair pathways in dividing cells. Homology-directed repair (HDR) of collapsed replication forks was proposed to repair SSBs in PNKP-deficient cells, but the critical HDR protein Rad51 is not required in PNKP-null (pnk1Δ) cells of Schizosaccharomyces pombe...
September 18, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28911793/passive-air-sampling-of-polybrominated-diphenyl-ethers-in-new-delhi-kolkata-mumbai-and-chennai-levels-homologous-profiling-and-source-apportionment
#4
Paromita Chakraborty, Gan Zhang, Hairong Cheng, Prithiviraj Balasubramanian, Jun Li, Kevin C Jones
Several studies in the recent past reported new sources for industrial persistent organic pollutants (POPs) from metropolitan cities of India. To fill the data gap for atmospheric polybrominated diphenyl ethers (PBDEs), polyurethane foam disk passive air sampling (PUF-PAS) was conducted along urban-suburban-rural transects in four quadrilateral cities viz., New Delhi, Kolkata, Mumbai and Chennai from northern, eastern, western and southern India respectively. Average concentration of Σ8PBDEs in pg/m(3) for New Delhi, Kolkata, Mumbai and Chennai were 198, 135, 264 and 144 respectively...
September 11, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28900805/mgmt-and-msh6-immunoexpression-for-functioning-pituitary-macroadenomas
#5
Alexander S G Micko, Adelheid Wöhrer, Romana Höftberger, Greisa Vila, Christine Marosi, Engelbert Knosp, Stefan Wolfsberger
PURPOSE: Knowledge of biological behavior is crucial for clinical management of functioning pituitary macroadenomas. For recurrent cases unresponsive to standard treatment, temozolomide (TMZ) has been used as a therapeutic alternative. MGMT (O6-methyl-guanine-DNA methyltransferase) and MSH6 (mutS homolog 6) immunoexpression have been linked to the response to TMZ treatment and MGMT immunoexpression has been additionally linked to early recurrence of non-functioning pituitary adenomas...
September 12, 2017: Pituitary
https://www.readbyqxmd.com/read/28892854/tissue-distribution-and-maternal-transfer-of-persistent-organic-pollutants-in-kentish-plovers-charadrius-alexandrines-from-cangzhou-wetland-bohai-bay-china
#6
Shucheng Zheng, Pu Wang, Huizhong Sun, Julius Matsiko, Yanfen Hao, Derong Meng, Yingming Li, Guogang Zhang, Qinghua Zhang, Guibin Jiang
Several persistent organic pollutants, including polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs), polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs) and organochlorine pesticides (OCPs), were comprehensively investigated in the egg, muscle and liver samples of Kentish Plover (Charadrius alexandrines) collected from Cangzhou Wetland in western Bohai Bay, China. DDTs were the most abundant contaminants (35.4-9853ngg(-1) lipid weight, lw), followed by HCHs, PCBs, PBDEs and HCB...
September 7, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28892294/nuclease-activity-gives-an-edge-to-host-defense-peptide-piscidin-3-over-piscidin-1-rendering-it-more-effective-against-persisters-and-biofilms
#7
M Daben J Libardo, Ali Adem Bahar, Buyong Ma, Riqiang Fu, Laura E McCormick, Jun Zhao, Scott A McCallum, Ruth Nussinov, Dacheng Ren, Alfredo M Angeles-Boza, Myriam L Cotten
Host defense peptides (HDPs) feature evolution-tested potency against life-threatening pathogens. While piscidin 1 (p1) and piscidin 3 (p3) are homologous and potent fish HDPs, only p1 is strongly membranolytic. Here, we hypothesize that another mechanism imparts p3 strong potency. We demonstrate that the N-termini of both peptides coordinate Cu(2+) and p3-Cu cleaves isolated DNA at a rate on par with free Cu(2+) but significantly faster than p1-Cu. On planktonic bacteria, p1 is more antimicrobial but only p3 features copper-dependent DNA cleavage...
September 11, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28890670/a-phenomenological-and-dynamic-view-of-homology-homologs-as-persistently-reproducible-modules
#8
Daichi G Suzuki, Senji Tanaka
Homology is a fundamental concept in biology. However, the metaphysical status of homology, especially whether a homolog is a part of an individual or a member of a natural kind, is still a matter of intense debate. The proponents of the individuality view of homology criticize the natural kind view of homology by pointing out that homologs are subject to evolutionary transformation, and natural kinds do not change in the evolutionary process. Conversely, some proponents of the natural kind view of homology argue that a homolog can be construed both as a part of an individual and a member of a natural kind...
2017: Biological Theory
https://www.readbyqxmd.com/read/28884202/gcg-creert2-knockin-mice-as-a-tool-for-genetic-manipulation-in-pancreatic-alpha-cells
#9
Chiyo Shiota, Krishna Prasadan, Ping Guo, Joseph Fusco, Xiangwei Xiao, George K Gittes
AIMS/HYPOTHESIS: The Cre/loxP system, which enables tissue-specific manipulation of genes, is widely used in mice for diabetes research. Our aim was to develop a new Cre-driver mouse line for the specific and efficient manipulation of genes in pancreatic alpha cells. METHODS: A Gcg (CreERT2) knockin mouse, which expresses a tamoxifen-inducible form of Cre from the endogenous preproglucagon (Gcg) gene locus, was generated by homologous recombination. The new Gcg (CreERT2) mouse line was crossed to the Rosa26 (tdTomato) (R26 (tdTomato) ) Cre reporter mouse line in order to evaluate the tissue specificity, efficiency and tamoxifen dependency of Gcg (CreERT2) -mediated recombination...
September 7, 2017: Diabetologia
https://www.readbyqxmd.com/read/28866539/clique-community-persistence-a-topological-visual-analysis-approach-for-complex-networks
#10
Bastian Rieck, Ulderico Fugacci, Jonas Lukasczyk, Heike Leitte
Complex networks require effective tools and visualizations for their analysis and comparison. Clique communities have been recognized as a powerful concept for describing cohesive structures in networks. We propose an approach that extends the computation of clique communities by considering persistent homology, a topological paradigm originally introduced to characterize and compare the global structure of shapes. Our persistence-based algorithm is able to detect clique communities and to keep track of their evolution according to different edge weight thresholds...
August 29, 2017: IEEE Transactions on Visualization and Computer Graphics
https://www.readbyqxmd.com/read/28864978/phase-ii-basket-trial-of-perifosine-monotherapy-for-recurrent-gynecologic-cancer-with-or-without-pik3ca-mutations
#11
Kosei Hasegawa, Masahiro Kagabu, Mika Mizuno, Katsutoshi Oda, Daisuke Aoki, Seiji Mabuchi, Shoji Kamiura, Satoshi Yamaguchi, Yoichi Aoki, Toshiaki Saito, Mayu Yunokawa, Kazuhiro Takehara, Aikou Okamoto, Kazunori Ochiai, Tadashi Kimura
Objective Perifosine exhibits anti-tumor activity by inhibiting AKT phosphorylation. The purpose of this phase II basket trial was to evaluate the efficacy and safety of perifosine monotherapy for ovarian, endometrial, and cervical cancers. Methods Recurrent or persistent ovarian, endometrial, or cervical cancer patients were assigned to PIK3CA wild-type or mutant groups. Each patient received 600 mg oral perifosine on day 1 followed by a maintenance dose of 100 mg daily. The primary endpoint was disease control rate; secondary endpoints included response rate, progression-free survival, overall survival, and safety...
September 2, 2017: Investigational New Drugs
https://www.readbyqxmd.com/read/28861401/micropathogen-community-analysis-in-hyalomma-rufipes-via-high-throughput-sequencing-of-small-rnas
#12
Jin Luo, Min-Xuan Liu, Qiao-Yun Ren, Ze Chen, Zhan-Cheng Tian, Jia-Wei Hao, Feng Wu, Xiao-Cui Liu, Jian-Xun Luo, Hong Yin, Hui Wang, Guang-Yuan Liu
Ticks are important vectors in the transmission of a broad range of micropathogens to vertebrates, including humans. Because of the role of ticks in disease transmission, identifying and characterizing the micropathogen profiles of tick populations have become increasingly important. The objective of this study was to survey the micropathogens of Hyalomma rufipes ticks. Illumina HiSeq2000 technology was utilized to perform deep sequencing of small RNAs (sRNAs) extracted from field-collected H. rufipes ticks in Gansu Province, China...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28859226/viral-persistence-liver-disease-and-host-response-in-hepatitis-c-like-virus-rat-model
#13
Sheetal Trivedi, Satyapramod Murthy, Himanshu Sharma, Alex S Hartlage, Arvind Kumar, Sashi Gadi, Peter Simmonds, Lokendra V Chauhan, Troels K H Scheel, Eva Billerbeck, Peter D Burbelo, Charles M Rice, W Ian Lipkin, Kurt Vandergrift, John M Cullen, Amit Kapoor
The lack of a relevant, tractable, and immunocompetent animal model for hepatitis C virus (HCV) has severely impeded investigations of viral persistence, immunity and pathogenesis. In the absence of immunocompetent models with robust HCV infection, homolog hepaciviruses in their natural host could potentially provide useful surrogate models. We isolated a rodent hepacivirus (RHV) from wild rats (Rattus norvegicus), RHV-rn1, acquired the complete viral genome sequence and developed an infectious reverse genetics system...
August 31, 2017: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/28846114/identification-of-translationally-controlled-tumor-protein-in-promotion-of-dna-homologous-recombination-repair-in-cancer-cells-by-affinity-proteomics
#14
Y Li, H Sun, C Zhang, J Liu, H Zhang, F Fan, R A Everley, X Ning, Y Sun, J Hu, J Liu, J Zhang, W Ye, X Qiu, S Dai, B Liu, H Xu, S Fu, S P Gygi, C Zhou
Translationally controlled tumor protein(TCTP) has been implicated in the regulation of apoptosis, DNA repair and drug resistance. However, the underlying molecular mechanisms are poorly defined. To better understand the molecular mechanisms underlying TCTP involved in cellular processes, we performed an affinity purification-based proteomic profiling to identify proteins interacting with TCTP in human cervical cancer HeLa cells. We found that a group of proteins involved in DNA repair are enriched in the potential TCTP interactome...
August 28, 2017: Oncogene
https://www.readbyqxmd.com/read/28844373/blood-derived-eye-drops-for-the-treatment-of-cornea-and-ocular-surface-diseases
#15
REVIEW
Giuseppe Giannaccare, Piera Versura, Marina Buzzi, Laura Primavera, Marco Pellegrini, Emilio C Campos
The use of blood derived eye drops for the treatment of ocular surface disorders has become increasingly popular in recent years. The mechanism of action is the stimulation of cellular proliferation and migration by supplying an active mixture of growth factors and cytokines at the ocular surface, thus mimicking the function of the lacking natural tears. Blood derived eye drops have been used in the last decades for the treatment of a variety of ocular surface diseases, including mainly dry eye disease, persistent corneal epithelial defect, corneal ulcer, ocular surface burn, recurrent corneal erosion and limbal stem-cell deficiency...
August 8, 2017: Transfusion and Apheresis Science
https://www.readbyqxmd.com/read/28814604/macrophage-restricted-shp2-tyrosine-phosphatase-acts-as-a-rheostat-for-mmp12-through-tgf-%C3%AE-activation-in-the-prevention-of-age-related-emphysema-in-mice
#16
Jiaqi Xu, Bo Tao, Xiaohong Guo, Shiyi Zhou, Yongda Li, Yuqin Zhang, Zanhua Zhou, Hongqiang Cheng, Xue Zhang, Yuehai Ke
Persistent activation of macrophages in lungs plays a critical role in the production of matrix metalloproteinases (MMPs) that contributes to the destruction of alveolar walls, a hallmark for pulmonary emphysema. Dysregulated TGF-β1 signaling has been an essential determinant in the elevation of MMPs during the development of emphysema. Nevertheless, the mechanism for this MMP-dependent pathogenesis has yet to be clearly investigated. Recently, we identified an important role for tyrosine phosphatase Src homology domain-containing protein tyrosine phosphatase 2 (Shp2) in regulating the activation of alveolar macrophages...
August 16, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28813660/neutralizing-antibody-responses-to-viral-infections-are-linked-to-the-non-classical-mhc-class-ii-gene-h2-ob
#17
Lisa K Denzin, Aly A Khan, Francesca Virdis, Jessica Wilks, Melissa Kane, Helen A Beilinson, Stanislav Dikiy, Laure K Case, Derry Roopenian, Michele Witkowski, Alexander V Chervonsky, Tatyana V Golovkina
Select humans and animals control persistent viral infections via adaptive immune responses that include production of neutralizing antibodies. The precise genetic basis for the control remains enigmatic. Here, we report positional cloning of the gene responsible for production of retrovirus-neutralizing antibodies in mice of the I/LnJ strain. It encodes the beta subunit of the non-classical major histocompatibility complex class II (MHC-II)-like molecule H2-O, a negative regulator of antigen presentation. The recessive and functionally null I/LnJ H2-Ob allele supported the production of virus-neutralizing antibodies independently of the classical MHC haplotype...
August 15, 2017: Immunity
https://www.readbyqxmd.com/read/28809960/metrics-for-comparing-neuronal-tree-shapes-based-on-persistent-homology
#18
Yanjie Li, Dingkang Wang, Giorgio A Ascoli, Partha Mitra, Yusu Wang
As more and more neuroanatomical data are made available through efforts such as NeuroMorpho.Org and FlyCircuit.org, the need to develop computational tools to facilitate automatic knowledge discovery from such large datasets becomes more urgent. One fundamental question is how best to compare neuron structures, for instance to organize and classify large collection of neurons. We aim to develop a flexible yet powerful framework to support comparison and classification of large collection of neuron structures efficiently...
2017: PloS One
https://www.readbyqxmd.com/read/28809399/evidence-for-newly-generated-interneurons-in-the-basolateral-amygdala-of-adult-mice
#19
D J Jhaveri, A Tedoldi, S Hunt, R Sullivan, N R Watts, J M Power, P F Bartlett, P Sah
New neurons are continually generated from the resident populations of precursor cells in selective niches of the adult mammalian brain such as the hippocampal dentate gyrus and the olfactory bulb. However, whether such cells are present in the adult amygdala, and their neurogenic capacity, is not known. Using the neurosphere assay, we demonstrate that a small number of precursor cells, the majority of which express Achaete-scute complex homolog 1 (Ascl1), are present in the basolateral amygdala (BLA) of the adult mouse...
August 15, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28783594/antigenic-characterization-of-52-55kda-protein-isolated-from-trypanosoma-evansi-and-its-application-in-detection-of-equine-trypanosomosis
#20
S C Yadav, Ritesh Kumar, Jaideep Kumar, Meetali Singh, B C Bera, Rajender Kumar, U Tatu, Kanika Tehri
Trypanosoma evansi is a haemo-protozoan parasite responsible for the disease surra, an economically important disease of wide range of domestic and wild animals. The present diagnostic methods using soluble antigens have inherent problems like lack of standardized and reproducible antigens, as well as ethical issues. This entails further efforts for search of defined antigenic molecules with satisfying sensitivity and specificity for sero-epidemiology of trypanosomosis. In present investigation, we have identified and purified 52-55kDa immuno-dominant protein cluster in molecular mass ranges by preparatory SDS-PAGE methods from T...
August 1, 2017: Research in Veterinary Science
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